Weeklies and red boxes, weeklies and red boxes, weeklies and red boxes.......... Just make every account have to pay 1m N-meseta to unlock the player shop, reduce the amount of N-meseta from weeklies, and increase N-meseta from one-time story quests.
Is it a minor inconvenience? Yes.
Does it drastically harm new players? No, 1m can be acquired on a single account after a fair bit of playing.
Does it cost more than what you get for red box farming? Yup, that's the point.
Why increase N-meseta from story quests? If the combined N-meseta from red boxes and story is enough for the 1m to unlock the player shop, then every new player can still have an easy way to unlock it. This covers for the reduction of N-meseta from weeklies, to function as a way to earn the 1m. But it means N-meseta from weeklies can be reduced enough to not make it worth it to farm them on multiple accounts.
Why not just remove N-meseta from red boxes and weeklies? This way it feels like people are still earning something. They are still earning N-meseta, and have something to work toward that they can unlock. This gives the feeling of forward progress, as opposed to everything in the game just not giving anything and not being worth it. Don't remove features, make them part of the progress.